Hi @all,
we are currently struggling with pros/cons of buying a PB sequel vs ONT Promethion for our analyses (human de novo single celll WGS). Ideally we are looking for something with which we can analyse structural variants and SNPs (so something with ~100Gb+ (>30x) output).
Unfortunately, we're getting extremely diverse information about the specifications of the two systems. Hence, I'd like to ask users of each system for info on their experience (I have therefore a similar post in the ONT forum).

My information on the sequel so far:
1) Accuracy of >99.999%
Is this a consensus acc from assembly/mapping? As this would be coverage dependent, it is meaningless for me... What about individual read (CCS) accuracy? I know there is something mentioned on the PB website, but I don't really understand their graph http://www.pacb.com/smrt-science/smr...cing/accuracy/

2) Output of ~5Gb per SMRT cell / ~800€ per SMRT cell run
So, I would need ~20 SMRT cells / genome => ~16k€ / genome? However, I have heard from colleagues who tested the system that a cost of 30-40k€ / genome would be more realistic for our aims?!

SMRT cell delivery schedule is ok, but its shelf-life, usually 1-2 months left after arrived. And although SMRT cells is 4 per tray for purchase, but the sequencing kit is one plate for 8 cells, allowing few days to use up the sequencing kit once opened.

My information on the sequel so far:
1) Accuracy of >99.999%
Is this a consensus acc from assembly/mapping? As this would be coverage dependent, it is meaningless for me... What about individual read (CCS) accuracy? I know there is something mentioned on the PB website, but I don't really understand their graph http://www.pacb.com/smrt-science/smr...cing/accuracy/

The graph indicates that the more coverage you have, the higher the quality of the self-corrected data (meaning reads corrected by other reads in the same library, not reads corrected by themselves). Last I saw, our RSII was producing 86-87% accurate reads and Sequel was producing 80-83% accurate reads, according to PacBio's software. CCS accuracy simply depends on how long the movie is compared to the insert size; for long insert libraries that you would generate for SV's, you would not yield many useful multi-pass CCS reads.